# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 04:04:20 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: 4-(2-methyl-1-benzofuran-5-yl)pyridine-2,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc2ccc(cc2c1)c3cc(N)nc(N)c3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 RKH  RKH  4-(2-methyl-1-benzofuran-5-yl)pyridine-2,6-diamine  ligand  31  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RKH
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 RKH  C1   C  CH3   0  -0.753  -24.6011  21.1011  -26.5532
 RKH  N1   N  NH2   0  -0.838  -19.3100  29.6826  -30.4285
 RKH  O1   O  O     0  -0.453  -24.5598  23.3265  -27.5034
 RKH  C2   C  CR5   0   0.370  -23.8563  22.3356  -26.8823
 RKH  N2   N  N     0  -0.506  -18.5323  29.0394  -28.3693
 RKH  C3   C  CR15  0  -0.428  -22.5701  22.7009  -26.6865
 RKH  N3   N  NH2   0  -0.838  -17.6630  28.4806  -26.3232
 RKH  C4   C  CR56  0   0.101  -22.4402  24.0284  -27.2200
 RKH  C5   C  CR56  0   0.344  -23.7068  24.3524  -27.7093
 RKH  C6   C  CR16  0  -0.329  -23.9982  25.5608  -28.3139
 RKH  C7   C  CR16  0  -0.319  -22.9553  26.4652  -28.4273
 RKH  C8   C  CR6   0   0.064  -21.6646  26.1793  -27.9476
 RKH  C9   C  CR16  0  -0.402  -21.4079  24.9549  -27.3383
 RKH  C10  C  CR6   0   0.200  -20.5829  27.1774  -28.0919
 RKH  C11  C  CR16  0  -0.489  -20.4777  27.9442  -29.2468
 RKH  C12  C  CR6   0   0.460  -19.4313  28.8696  -29.3368
 RKH  C13  C  CR6   0   0.459  -18.6357  28.3019  -27.2656
 RKH  C14  C  CR16  0  -0.487  -19.6517  27.3573  -27.0760
 RKH  H1   H  HCH3  0   0.260  -25.4310  21.3052  -25.8742
 RKH  H2   H  HCH3  0   0.260  -25.0144  20.6332  -27.4483
 RKH  H3   H  HCH3  0   0.261  -23.9371  20.3868  -26.0718
 RKH  H4   H  HNH2  0   0.377  -18.4027  30.0938  -30.5751
 RKH  H5   H  HNH2  0   0.385  -19.7659  29.3872  -31.2758
 RKH  H6   H  HCR5  0   0.261  -21.8074  22.0993  -26.2185
 RKH  H7   H  HNH2  0   0.377  -17.1528  29.3473  -26.3703
 RKH  H8   H  HNH2  0   0.386  -17.8637  28.1723  -25.3865
 RKH  H9   H  HCR6  0   0.268  -24.9898  25.7972  -28.6767
 RKH  H10  H  HCR6  0   0.256  -23.1503  27.4279  -28.8817
 RKH  H11  H  HCR6  0   0.254  -20.4146  24.7156  -26.9799
 RKH  H12  H  HCR6  0   0.249  -21.1657  27.8170  -30.0725
 RKH  H13  H  HCR6  0   0.250  -19.7122  26.8021  -26.1489

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 RKH  N1   C12  single    1.367  0.020  1.367
 RKH  C12  C11  aromatic  1.400  0.020  1.400
 RKH  C12  N2   aromatic  1.332  0.020  1.332
 RKH  C11  C10  aromatic  1.390  0.020  1.390
 RKH  C7   C6   aromatic  1.385  0.020  1.385
 RKH  C7   C8   aromatic  1.406  0.020  1.406
 RKH  C6   C5   aromatic  1.382  0.020  1.382
 RKH  N2   C13  aromatic  1.332  0.020  1.332
 RKH  C10  C8   single    1.479  0.020  1.479
 RKH  C10  C14  aromatic  1.390  0.020  1.390
 RKH  C8   C9   aromatic  1.392  0.020  1.392
 RKH  C5   O1   aromatic  1.350  0.020  1.350
 RKH  C5   C4   aromatic  1.396  0.020  1.396
 RKH  O1   C2   aromatic  1.365  0.020  1.365
 RKH  C13  C14  aromatic  1.400  0.020  1.400
 RKH  C13  N3   single    1.366  0.020  1.366
 RKH  C9   C4   aromatic  1.392  0.020  1.392
 RKH  C4   C3   aromatic  1.437  0.020  1.437
 RKH  C2   C3   aromatic  1.351  0.020  1.351
 RKH  C2   C1   single    1.479  0.020  1.479
 RKH  C1   H1   single    0.970  0.020  1.090
 RKH  C1   H2   single    0.970  0.020  1.090
 RKH  C1   H3   single    0.970  0.020  1.090
 RKH  N1   H4   single    0.890  0.020  1.040
 RKH  N1   H5   single    0.890  0.020  1.040
 RKH  C3   H6   single    0.930  0.020  1.080
 RKH  N3   H7   single    0.890  0.020  1.040
 RKH  N3   H8   single    0.890  0.020  1.040
 RKH  C6   H9   single    0.930  0.020  1.080
 RKH  C7   H10  single    0.930  0.020  1.080
 RKH  C9   H11  single    0.930  0.020  1.080
 RKH  C11  H12  single    0.930  0.020  1.080
 RKH  C14  H13  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 RKH  H3   C1   H2   108.22  3.000
 RKH  H3   C1   H1   108.15  3.000
 RKH  H2   C1   H1   107.60  3.000
 RKH  H3   C1   C2   109.83  3.000
 RKH  H2   C1   C2   111.48  3.000
 RKH  H1   C1   C2   111.43  3.000
 RKH  H5   N1   H4   113.92  3.000
 RKH  H5   N1   C12  117.24  3.000
 RKH  H4   N1   C12  116.05  3.000
 RKH  C5   O1   C2   107.19  3.000
 RKH  C3   C2   O1   111.12  3.000
 RKH  C3   C2   C1   132.28  3.000
 RKH  O1   C2   C1   116.60  3.000
 RKH  C13  N2   C12  118.63  3.000
 RKH  H6   C3   C4   127.79  3.000
 RKH  H6   C3   C2   125.83  3.000
 RKH  C4   C3   C2   106.39  3.000
 RKH  H8   N3   H7   114.10  3.000
 RKH  H8   N3   C13  117.39  3.000
 RKH  H7   N3   C13  116.18  3.000
 RKH  C9   C4   C5   119.24  3.000
 RKH  C9   C4   C3   135.53  3.000
 RKH  C5   C4   C3   105.22  3.000
 RKH  C6   C5   C4   123.19  3.000
 RKH  C4   C5   O1   110.09  3.000
 RKH  C6   C5   O1   126.72  3.000
 RKH  H9   C6   C7   121.33  3.000
 RKH  H9   C6   C5   122.06  3.000
 RKH  C7   C6   C5   116.61  3.000
 RKH  H10  C7   C8   119.30  3.000
 RKH  H10  C7   C6   118.65  3.000
 RKH  C8   C7   C6   122.03  3.000
 RKH  C10  C8   C9   120.11  3.000
 RKH  C9   C8   C7   119.83  3.000
 RKH  C10  C8   C7   120.05  3.000
 RKH  H11  C9   C8   120.58  3.000
 RKH  H11  C9   C4   120.33  3.000
 RKH  C8   C9   C4   119.08  3.000
 RKH  C14  C10  C11  119.02  3.000
 RKH  C14  C10  C8   120.40  3.000
 RKH  C11  C10  C8   120.57  3.000
 RKH  H12  C11  C12  120.25  3.000
 RKH  H12  C11  C10  121.39  3.000
 RKH  C12  C11  C10  118.33  3.000
 RKH  C11  C12  N2   122.84  3.000
 RKH  N2   C12  N1   116.40  3.000
 RKH  C11  C12  N1   120.73  3.000
 RKH  C14  C13  N3   120.77  3.000
 RKH  N3   C13  N2   116.36  3.000
 RKH  C14  C13  N2   122.84  3.000
 RKH  H13  C14  C13  120.18  3.000
 RKH  H13  C14  C10  121.48  3.000
 RKH  C13  C14  C10  118.33  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 RKH  CONST_01  C7   C6   C5   O1   180.00   0.0  0
 RKH  CONST_02  C9   C4   C5   O1   180.00   0.0  0
 RKH  CONST_03  C3   C4   C5   O1     0.00   0.0  0
 RKH  CONST_04  C4   C3   C2   O1     0.00   0.0  0
 RKH  CONST_05  C6   C5   O1   C2   180.00   0.0  0
 RKH  CONST_06  C4   C5   O1   C2     0.00   0.0  0
 RKH  CONST_07  C5   C4   C3   C2     0.00   0.0  0
 RKH  CONST_08  C9   C4   C3   C2   180.00   0.0  0
 RKH  CONST_09  C10  C11  C12  N2     0.00   0.0  0
 RKH  CONST_10  C10  C14  C13  N2     0.00   0.0  0
 RKH  CONST_11  C6   C5   C4   C3   180.00   0.0  0
 RKH  CONST_12  C8   C9   C4   C3   180.00   0.0  0
 RKH  CONST_13  C5   O1   C2   C3     0.00   0.0  0
 RKH  CONST_14  C7   C6   C5   C4     0.00   0.0  0
 RKH  CONST_15  C7   C8   C9   C4     0.00   0.0  0
 RKH  CONST_16  C10  C8   C9   C4   180.00   0.0  0
 RKH  CONST_17  C8   C7   C6   C5     0.00   0.0  0
 RKH  CONST_18  C8   C9   C4   C5     0.00   0.0  0
 RKH  CONST_19  C10  C8   C7   C6   180.00   0.0  0
 RKH  CONST_20  C9   C8   C7   C6     0.00   0.0  0
 RKH  CONST_21  C9   C4   C5   C6     0.00   0.0  0
 RKH  CONST_24  C12  C11  C10  C8   180.00   0.0  0
 RKH  CONST_25  C13  C14  C10  C8   180.00   0.0  0
 RKH  CONST_28  C13  N2   C12  C11    0.00   0.0  0
 RKH  CONST_29  C13  C14  C10  C11    0.00   0.0  0
 RKH  CONST_30  C14  C10  C11  C12    0.00   0.0  0
 RKH  CONST_31  C14  C13  N2   C12    0.00   0.0  0
 RKH  CONST_32  C5   O1   C2   C1   180.00   0.0  0
 RKH  CONST_33  C4   C3   C2   C1   180.00   0.0  0
 RKH  CONST_34  C10  C11  C12  N1   180.00   0.0  0
 RKH  CONST_35  C13  N2   C12  N1   180.00   0.0  0
 RKH  CONST_36  C12  N2   C13  N3   180.00   0.0  0
 RKH  CONST_37  C10  C14  C13  N3   180.00   0.0  0
 RKH  CONST_38  H9   C6   C5   O1     0.00   0.0  0
 RKH  CONST_39  H6   C3   C2   O1   180.00   0.0  0
 RKH  CONST_40  H12  C11  C12  N2   180.00   0.0  0
 RKH  CONST_41  H13  C14  C13  N2   180.00   0.0  0
 RKH  CONST_42  H11  C9   C4   C3     0.00   0.0  0
 RKH  CONST_43  H10  C7   C6   C5   180.00   0.0  0
 RKH  Var_01    H1   C1   C2   O1   -60.64  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 RKH  plan-1  N1   0.020
 RKH  plan-1  N2   0.020
 RKH  plan-1  N3   0.020
 RKH  plan-1  C8   0.020
 RKH  plan-1  C10  0.020
 RKH  plan-1  C11  0.020
 RKH  plan-1  C12  0.020
 RKH  plan-1  C13  0.020
 RKH  plan-1  C14  0.020
 RKH  plan-1  H12  0.020
 RKH  plan-1  H13  0.020
 RKH  plan-2  C1   0.020
 RKH  plan-2  O1   0.020
 RKH  plan-2  C2   0.020
 RKH  plan-2  C3   0.020
 RKH  plan-2  C4   0.020
 RKH  plan-2  C5   0.020
 RKH  plan-2  C6   0.020
 RKH  plan-2  C7   0.020
 RKH  plan-2  C8   0.020
 RKH  plan-2  C9   0.020
 RKH  plan-2  C10  0.020
 RKH  plan-2  H6   0.020
 RKH  plan-2  H9   0.020
 RKH  plan-2  H10  0.020
 RKH  plan-2  H11  0.020
 RKH  plan-3  N1   0.020
 RKH  plan-3  C12  0.020
 RKH  plan-3  H4   0.020
 RKH  plan-3  H5   0.020
 RKH  plan-4  N3   0.020
 RKH  plan-4  C13  0.020
 RKH  plan-4  H7   0.020
 RKH  plan-4  H8   0.020

